Use Ruff for Python linting and formatting

This replaces the black, pyupgrade, reorder-python-imports and flake8
hooks in pre-commit with ruff.

.pre-commit-config.yaml

@@ -1,26 +1,10 @@
 repos:
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.16.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.9
   hooks:
-  - id: pyupgrade
-    args: [--py38-plus]
-- repo: https://github.com/asottile/reorder_python_imports
-  rev: v3.13.0
-  hooks:
-  - id: reorder-python-imports
-    args: [--py38-plus]
-- repo: https://github.com/psf/black
-  rev: "23.12.1"
-  hooks:
-  - id: black
-    args: [--safe, --quiet]
-- repo: https://github.com/pycqa/flake8
-  rev: "7.1.0"
-  hooks:
-  - id: flake8
-    additional_dependencies:
-    - flake8-bugbear==24.4.26
-    - flake8-comprehensions==3.14.0
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+  - id: ruff-format
 - repo: https://github.com/igorshubovych/markdownlint-cli
   rev: v0.41.0
   hooks:

aips/create_dip.py

@@ -11,6 +11,7 @@
 generated alongside the objects folder containing only a reference to the ZIP file
 (without AMD or DMD sections).
 """
+
 import argparse
 import csv
 import logging.config  # Has to be imported separately

aips/create_dips_job.py

@@ -9,6 +9,7 @@
 Optionally, uploads those DIPs to AtoM or the Storage Service using
 the scripts from `dips` and deletes the local copy.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os

aips/models.py

@@ -1,10 +1,10 @@
 from os.path import isfile
 
 from sqlalchemy import Column
-from sqlalchemy import create_engine
 from sqlalchemy import Integer
 from sqlalchemy import Sequence
 from sqlalchemy import String
+from sqlalchemy import create_engine
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
 

dips/atom_upload.py

@@ -6,6 +6,7 @@
 AtoM instance. A passwordless SSH connection is required to the AtoM host for the
 user running this script and it must be already added to the list of known hosts.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os
@@ -15,7 +16,6 @@
 
 import requests
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("dip_workflow")
 

dips/copy_to_netx.py

@@ -4,6 +4,7 @@
 
 Copies a local DIP to NetX, providing a CSV list of each object.
 """
+
 import argparse
 import csv
 import logging.config  # Has to be imported separately
@@ -14,7 +15,6 @@
 
 import lxml.etree
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("copy_to_netx")
 

dips/storage_service_upload.py

@@ -8,6 +8,7 @@
 Storage Service to process that DIP and create a relationship with the
 AIP from where it was created.
 """
+
 import argparse
 import logging.config  # Has to be imported separately
 import os
@@ -17,7 +18,6 @@
 
 import requests
 
-
 THIS_DIR = os.path.abspath(os.path.dirname(__file__))
 LOGGER = logging.getLogger("dip_workflow")
 

requirements-dev.in

@@ -1,3 +1,4 @@
 -r requirements.txt
 pytest
 pytest-cov
+ruff

requirements-dev.txt

@@ -48,6 +48,8 @@ requests==2.32.3
     # via
     #   -r requirements.txt
     #   amclient
+ruff==0.4.9
+    # via -r requirements-dev.in
 sqlalchemy==1.4.52
     # via -r requirements.txt
 tomli==2.0.1

ruff.toml

@@ -0,0 +1,19 @@
+[lint]
+# Rule reference: https://docs.astral.sh/ruff/rules/
+select = [
+  "B",
+  "C4",
+  "E",
+  "F",
+  "I",
+  "UP",
+  "W",
+]
+ignore = [
+  "B904",
+  "E501",
+  "UP031",
+]
+
+[lint.isort]
+force-single-line = true

tests/test_create_avalon_dip.py

@@ -9,7 +9,6 @@
 
 from aips import create_dip
 
-
 SS_URL = "http://127.0.0.1:62081"
 SS_USER_NAME = "test"
 SS_API_KEY = "test"
@@ -68,8 +67,8 @@ def test_create_avalon_dip_success(_get, tmp_path):
         aip_dir, AVALON_AIP_UUID, output_dir.as_posix(), "atom", "avalon-manifest"
     )
     # Check DIP structure
-    assert avalon_dip_dir == "{}/{}/{}".format(
-        output_dir.as_posix(), TRANSFER_NAME, AVALON_AIP_UUID
+    assert (
+        avalon_dip_dir == f"{output_dir.as_posix()}/{TRANSFER_NAME}/{AVALON_AIP_UUID}"
     )
     assert os.path.isdir(avalon_dip_dir)
 

tests/test_create_dip.py

@@ -10,7 +10,6 @@
 
 from aips import create_dip
 
-
 SS_URL = "http://192.168.168.192:8000"
 SS_USER_NAME = "test"
 SS_API_KEY = "7021334bee4c9155c07e531608dd28a9d8039420"

tests/test_create_dips_job.py

@@ -9,7 +9,6 @@
 
 from aips import create_dips_job
 
-
 SS_URL = "http://192.168.168.192:8000"
 SS_USER_NAME = "test"
 SS_API_KEY = "12883879c823f6e533738c12266bfe9f7316a672"
@@ -149,7 +148,7 @@ def test_main_fail_request(_request, args):
                 ),
                 "json.return_value": AIPS_JSON,
             },
-            spec=requests.Response
+            spec=requests.Response,
         )
     ],
 )
@@ -162,7 +161,7 @@ def test_main_fail_request(_request, args):
                 "headers": {},
                 "iter_content.return_value": iter([AIP_CONTENT]),
             },
-            spec=requests.Response
+            spec=requests.Response,
         ),
     ],
 )
@@ -187,7 +186,7 @@ def test_main_success(_get, _request, args):
                 ),
                 "json.return_value": AIPS_JSON,
             },
-            spec=requests.Response
+            spec=requests.Response,
         )
     ],
 )
@@ -200,7 +199,7 @@ def test_main_success(_get, _request, args):
                 "headers": {},
                 "iter_content.return_value": iter([AIP_CONTENT]),
             },
-            spec=requests.Response
+            spec=requests.Response,
         ),
     ],
 )
@@ -230,7 +229,7 @@ def test_main_success_no_dip_creation(_get, _request, args):
                 ),
                 "json.return_value": AIPS_JSON,
             },
-            spec=requests.Response
+            spec=requests.Response,
         )
     ],
 )
@@ -243,7 +242,7 @@ def test_main_success_no_dip_creation(_get, _request, args):
                 "headers": {},
                 "iter_content.return_value": iter([AIP_CONTENT]),
             },
-            spec=requests.Response
+            spec=requests.Response,
         ),
     ],
 )
@@ -267,7 +266,7 @@ def test_main_dip_creation_failed(_get, _request, create_dip, atom_upload, args)
                 ),
                 "json.return_value": AIPS_JSON,
             },
-            spec=requests.Response
+            spec=requests.Response,
         )
     ],
 )
@@ -280,7 +279,7 @@ def test_main_dip_creation_failed(_get, _request, create_dip, atom_upload, args)
                 "headers": {},
                 "iter_content.return_value": iter([AIP_CONTENT]),
             },
-            spec=requests.Response
+            spec=requests.Response,
         ),
     ],
 )
@@ -314,7 +313,7 @@ def test_main_success_atom_upload_call(_get, _request, create_dip, atom_upload,
                 ),
                 "json.return_value": AIPS_JSON,
             },
-            spec=requests.Response
+            spec=requests.Response,
         )
     ],
 )
@@ -327,7 +326,7 @@ def test_main_success_atom_upload_call(_get, _request, create_dip, atom_upload,
                 "headers": {},
                 "iter_content.return_value": iter([AIP_CONTENT]),
             },
-            spec=requests.Response
+            spec=requests.Response,
         ),
     ],
 )

tests/test_storage_service_upload.py

@@ -88,7 +88,7 @@ def test_request_fail(self, _get, _makedirs, _copytree):
                     "json.return_value": {},
                     "headers": {},
                 },
-                spec=requests.Response
+                spec=requests.Response,
             )
         ],
     )

tests/test_transfers.py

@@ -10,7 +10,6 @@
 from transfers import models
 from transfers import transfer
 
-
 AM_URL = "http://127.0.0.1"
 SS_URL = "http://127.0.0.1:8000"
 USER = "demo"
@@ -42,17 +41,13 @@ def setUp(self):
                 transfer_type="standard",
                 target="standard_1",
                 transfer_name="standard_1",
-                transfer_abs_path="{}/standardTransfer/standard_1/".format(
-                    transfers_dir
-                ),
+                transfer_abs_path=f"{transfers_dir}/standardTransfer/standard_1/",
             ),
             Result(
                 transfer_type="standard",
                 target="standard_1",
                 transfer_name="standard_1_1",
-                transfer_abs_path="{}/standardTransfer/standard_1_1/".format(
-                    transfers_dir
-                ),
+                transfer_abs_path=f"{transfers_dir}/standardTransfer/standard_1_1/",
             ),
             Result(
                 transfer_type="dspace",

tests/test_transfers_async.py

@@ -7,7 +7,6 @@
 from transfers import models
 from transfers import transfer_async
 
-
 AM_URL = "http://127.0.0.1:62080"
 SS_URL = "http://127.0.0.1:62081"
 USER = "test"

transfers/defaults.py

@@ -11,7 +11,7 @@
 UNDECODABLE = "UNABLE TO DECODE"
 UNDEC_MSG = (
     "Unable to decode a transfer source component; giving up and"
-    " returning {}".format(UNDECODABLE)
+    f" returning {UNDECODABLE}"
 )
 
 # Default logging for thee module.

transfers/examples/split_transfer.py

@@ -13,6 +13,7 @@
 
 Make sure that you have permissions on the locations you are reading or writing!
 """
+
 import argparse
 import csv
 import os

transfers/models.py

@@ -1,10 +1,10 @@
 from sqlalchemy import Boolean
 from sqlalchemy import Column
-from sqlalchemy import create_engine
 from sqlalchemy import Integer
 from sqlalchemy import LargeBinary
 from sqlalchemy import Sequence
 from sqlalchemy import String
+from sqlalchemy import create_engine
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import scoped_session
 from sqlalchemy.orm import sessionmaker
@@ -29,8 +29,8 @@ class Unit(Base):
 
     def __repr__(self):
         return (
-            "<Unit(id={s.id}, uuid={s.uuid}, unit_type={s.unit_type}, "
-            "path={s.path}, status={s.status}, current={s.current})>".format(s=self)
+            f"<Unit(id={self.id}, uuid={self.uuid}, unit_type={self.unit_type}, "
+            f"path={self.path}, status={self.status}, current={self.current})>"
         )
 
 

transfers/reingest.py

@@ -8,6 +8,7 @@
 A work in progress, with some improvements that can be made to long-running
 processes like this over time.
 """
+
 import argparse
 import atexit
 import json
@@ -22,7 +23,8 @@
 # by ensuring that it can see itself.
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
-from transfers import errors, loggingconfig
+from transfers import errors
+from transfers import loggingconfig
 from transfers import reingestmodel as reingestunit
 
 LOGGER = logging.getLogger("transfers")